Reasons

The eds.reason matcher uses a rule-based algorithm to detect spans that relate to the reason of the hospitalisation. It was designed at AP-HP's EDS.

Examples

The following snippet matches a simple terminology, and looks for spans of hospitalisation reasons. It is complete and can be run as is.

import edsnlp, edsnlp.pipes as eds

text = """COMPTE RENDU D'HOSPITALISATION du 11/07/2018 au 12/07/2018
MOTIF D'HOSPITALISATION
Monsieur Dupont Jean Michel, de sexe masculin, âgée de 39 ans, née le 23/11/1978,
a été hospitalisé du 11/08/2019 au 17/08/2019 pour attaque d'asthme.

ANTÉCÉDENTS
Antécédents médicaux :
Premier épisode d'asthme en mai 2018."""

nlp = edsnlp.blank("eds")

# Extraction of entities
nlp.add_pipe(
    eds.matcher(
        terms=dict(
            respiratoire=[
                "asthmatique",
                "asthme",
                "toux",
            ]
        )
    ),
)
nlp.add_pipe(eds.normalizer())
nlp.add_pipe(eds.reason(use_sections=True))
doc = nlp(text)

reason = doc.spans["reasons"][0]
reason
# Out: hospitalisé du 11/08/2019 au 17/08/2019 pour attaque d'asthme.

reason._.is_reason
# Out: True

entities = reason._.ents_reason
entities
# Out: [asthme]

entities[0].label_
# Out: 'respiratoire'

ent = entities[0]
ent._.is_reason
# Out: True

Extensions

The eds.reason pipeline adds the key reasons to doc.spans and declares one extension, on the Span objects called ents_reason.

The ents_reason extension is a list of named entities that overlap the Span, typically entities found in upstream components like matcher.

It also declares the boolean extension is_reason. This extension is set to True for the Reason Spans but also for the entities that overlap the reason span.

Parameters

PARAMETER	DESCRIPTION
`nlp`	The pipeline object TYPE: `PipelineProtocol`
`name`	Name of the component TYPE: `str` DEFAULT: `'reason'`
`reasons`	Reason patterns TYPE: `Dict[str, Union[List[str], str]]` DEFAULT: `None`
`attr`	Default token attribute to use to build the text to match on. TYPE: `str` DEFAULT: `TEXT`
`use_sections`	Whether or not use the `sections` matcher to improve results. TYPE: `(bool)` DEFAULT: `False`
`ignore_excluded`	Whether to skip excluded tokens. TYPE: `bool` DEFAULT: `False`

Authors and citation

The eds.reason matcher was developed by AP-HP's Data Science team.